Added analysis of WSN H1 HA for eLife revision

docs/example_2014Analysis_Influenza_H1_HA.rst

@@ -5,8 +5,6 @@
 .. contents::
    :depth: 3
 
-**This description of the analysis is currently available. The actual source code and data for this specific analysis are not yet posted publicly on GitHub in the ``./examples/2014Analysis_Influenza_H1_HA/`` subdirectory. They will be posted upon publication of the paper. If you are a reviewer and you would like to see them now, please relay this request to Jesse via the editor.**
-
 Overview
 ------------
 This is an analysis of influenza A virus H1 hemagglutinins (HAs) from human and swine that are descended from a common ancestor closely related the HA of the 1918 virus. This analysis constructs phylogenies of these sequences and analyzes them with standard and experimentally determined codon substitution models.
@@ -34,13 +32,13 @@ The specific versions of software used are specified. Other versions will likely
 
 * `Python`_ (version 2.7.3)
 
-* `phyloExpCM`_ (version 0.21).
+* `phyloExpCM`_ (specifically, `phyloExpCM version 0.31`_).
 
 * `numpy`_ (version 1.6.1)
 
 * `matplotlib`_ (version 1.3.1).
 
-* `mapmuts`_ (version 1.0)
+* `mapmuts`_ (specifically, `mapmuts version 1.01`_)
 
 * `Biopython`_ (version 1.5.8)
 
@@ -382,3 +380,5 @@ The models are ranked in order of `AIC`_ difference from the best model. Both tr
 .. _`mapmuts analysis of the WSN HA from 2014` :  http://jbloom.github.io/mapmuts/example_WSN_HA_2014Analysis.html
 .. _`weblogo`: http://weblogo.threeplusone.com/
 .. _`pyPdf`: http://pybrary.net/pyPdf/
+.. _`phyloExpCM version 0.31`: https://github.com/jbloom/phyloExpCM/tree/v0.31
+.. _`mapmuts version 1.01`: https://github.com/jbloom/mapmuts/tree/v1.01

examples/2014Analysis_Influenza_H1_HA/.gitignore

@@ -0,0 +1,11 @@
+slurm*
+*.DS_Store
+*.fasta.reduced
+*sbatch*
+*replicate*logoplot*
+evolutionary_frequencies/*correlationplot*
+evolutionary_frequencies/*entropy_plot*
+messages.log
+errors.log
+*.swp
+._*

examples/2014Analysis_Influenza_H1_HA/CodonPhyML_Tree_H1_HumanSwine_GY94/codonphyml_config.drw

@@ -0,0 +1,19 @@
+cpconfig := table();
+cpconfig['inputfile'] := '/loc/scratch/6027413/tmp33pENBphylip';
+cpconfig['oformat'] := 'txt';
+cpconfig['sequential'] := true;
+cpconfig['multiple'] := 1;
+cpconfig['bootstrap'] := -4;
+cpconfig['search'] := 'NNI';
+cpconfig['optimize'] := 'tlr';
+cpconfig['quiet'] := true;
+cpconfig['modrates'] := true;
+cpconfig['r_seed'] := 1;
+cpconfig['datatype'] := 'codon';
+cpconfig['model'] := 'GY';
+cpconfig['frequencies'] := 'empirical';
+cpconfig['fmodel'] := 'CF3X4';
+cpconfig['kappa'] := 'e';
+cpconfig['omega'] := 'DGAMMA';
+cpconfig['wclasses'] := 4;
+cpconfig['alpha'] := 'e';

examples/2014Analysis_Influenza_H1_HA/CodonPhyML_Tree_H1_HumanSwine_GY94/codonphyml_loglikelihood.txt

@@ -0,0 +1 @@
+-24616.1

examples/2014Analysis_Influenza_H1_HA/CodonPhyML_Tree_H1_HumanSwine_GY94/phyloExpCM_runcodonphyml_infile.txt

@@ -0,0 +1,6 @@
+# input file for running script phyloExpCM_runcodonPhyML.py for phyloExpCM_runcodonphyml
+seqfile /home/jbloom/phyloExpCM/examples/2014Analysis_Influenza_H1_HA/H1_HumanSwine_alignment.fasta
+codonPhyML_path codonphyml
+seed 1
+outprefix codonphyml
+model GY94_CF3x4_omega-gamma4

examples/2014Analysis_Influenza_H1_HA/CodonPhyML_Tree_H1_HumanSwine_KOSI07/codonphyml_config.drw

@@ -0,0 +1,20 @@
+cpconfig := table();
+cpconfig['inputfile'] := '/loc/scratch/6027411/tmpwUVvFrphylip';
+cpconfig['oformat'] := 'txt';
+cpconfig['sequential'] := true;
+cpconfig['multiple'] := 1;
+cpconfig['bootstrap'] := -4;
+cpconfig['search'] := 'NNI';
+cpconfig['optimize'] := 'tlr';
+cpconfig['quiet'] := true;
+cpconfig['modrates'] := true;
+cpconfig['r_seed'] := 1;
+cpconfig['datatype'] := 'codon';
+cpconfig['model'] := 'GY';
+cpconfig['qrates'] := 'KOSI07';
+cpconfig['frequencies'] := 'empirical';
+cpconfig['fmodel'] := 'F1XCODONS';
+cpconfig['kappa'] := 'KAP3';
+cpconfig['omega'] := 'DGAMMA';
+cpconfig['wclasses'] := 4;
+cpconfig['alpha'] := 'e';

examples/2014Analysis_Influenza_H1_HA/CodonPhyML_Tree_H1_HumanSwine_KOSI07/codonphyml_loglikelihood.txt

@@ -0,0 +1 @@
+-24956.7

examples/2014Analysis_Influenza_H1_HA/CodonPhyML_Tree_H1_HumanSwine_KOSI07/phyloExpCM_runcodonphyml_infile.txt

@@ -0,0 +1,6 @@
+# input file for running script phyloExpCM_runcodonPhyML.py for phyloExpCM_runcodonphyml
+seqfile /home/jbloom/phyloExpCM/examples/2014Analysis_Influenza_H1_HA/H1_HumanSwine_alignment.fasta
+codonPhyML_path codonphyml
+seed 1
+outprefix codonphyml
+model KOSI07_F_omega-gamma4

examples/2014Analysis_Influenza_H1_HA/H1_HumanSwine_GY94_summary.csv

@@ -0,0 +1,27 @@
+#Summary for tree H1_HumanSwine_GY94.
+#
+#SUBSTITUTION_MODEL, dAIC, LOG_LIKELIHOOD, FREE_PARAMETERS, MAXIMUM_LIKELIHOOD_PARAMETERS, EMPIRICAL_PARAMETERS
+combined-FracTolerated, 0, -24088.7, 0, 0, 0
+replicate_3-FracTolerated, 303.2, -24240.3, 0, 0, 0
+combined-HalpernBruno, 500.6, -24339, 0, 0, 0
+replicate_1-FracTolerated, 535.4, -24356.4, 0, 0, 0
+replicate_3-HalpernBruno, 657.8, -24417.6, 0, 0, 0
+replicate_2-FracTolerated, 876.2, -24526.8, 0, 0, 0
+GY94_CF3x4_omega-global-gamma4_rates-gamma4, 882.573, -24517, 13, 4, 9
+replicate_1-HalpernBruno, 983.2, -24580.3, 0, 0, 0
+GY94_CF3x4_omega-global-gamma4_rates-one, 1109.67, -24631.5, 12, 3, 9
+replicate_2-HalpernBruno, 1190, -24683.7, 0, 0, 0
+KOSI07_F_omega-global-gamma4_rates-gamma4, 1620.45, -24834.9, 64, 4, 60
+GY94_CF3x4_omega-global-one_rates-gamma4, 1859.37, -25006.4, 12, 3, 9
+KOSI07_F_omega-global-gamma4_rates-one, 1883, -24967.2, 63, 3, 60
+KOSI07_F_omega-global-one_rates-gamma4, 2378.83, -25215.1, 63, 3, 60
+GY94_CF3x4_omega-global-one_rates-one, 2544.53, -25350, 11, 2, 9
+KOSI07_F_omega-global-one_rates-one, 3039.97, -25546.7, 62, 2, 60
+combined-FracToleratedrandomized, 5632.8, -26905.1, 0, 0, 0
+replicate_1-FracToleratedrandomized, 6002.4, -27089.9, 0, 0, 0
+replicate_3-FracToleratedrandomized, 6138.8, -27158.1, 0, 0, 0
+replicate_2-FracToleratedrandomized, 6477.8, -27327.6, 0, 0, 0
+combined-HalpernBrunorandomized, 7072.8, -27625.1, 0, 0, 0
+replicate_1-HalpernBrunorandomized, 7795, -27986.2, 0, 0, 0
+replicate_3-HalpernBrunorandomized, 7891.8, -28034.6, 0, 0, 0
+replicate_2-HalpernBrunorandomized, 8494.4, -28335.9, 0, 0, 0

examples/2014Analysis_Influenza_H1_HA/H1_HumanSwine_GY94_summary.tex

@@ -0,0 +1,27 @@
+\begin{tabular}{c|c|c|c}
+model & $\Delta$AIC & log likelihood & \parbox[b]{0.9in}{\center parameters (optimized + empirical)} \\ \hline
+combined-FracTolerated & 0.0 & -24088.7 & 0 (0 + 0) \\ 
+replicate 3-FracTolerated & 303.2 & -24240.3 & 0 (0 + 0) \\ 
+combined-HalpernBruno & 500.6 & -24339.0 & 0 (0 + 0) \\ 
+replicate 1-FracTolerated & 535.4 & -24356.4 & 0 (0 + 0) \\ 
+replicate 3-HalpernBruno & 657.8 & -24417.6 & 0 (0 + 0) \\ 
+replicate 2-FracTolerated & 876.2 & -24526.8 & 0 (0 + 0) \\ 
+GY94 CF3x4 omega-global-gamma4 rates-gamma4 & 882.6 & -24517.0 & 13 (4 + 9) \\ 
+replicate 1-HalpernBruno & 983.2 & -24580.3 & 0 (0 + 0) \\ 
+GY94 CF3x4 omega-global-gamma4 rates-one & 1109.7 & -24631.5 & 12 (3 + 9) \\ 
+replicate 2-HalpernBruno & 1190.0 & -24683.7 & 0 (0 + 0) \\ 
+KOSI07 F omega-global-gamma4 rates-gamma4 & 1620.5 & -24834.9 & 64 (4 + 60) \\ 
+GY94 CF3x4 omega-global-one rates-gamma4 & 1859.4 & -25006.4 & 12 (3 + 9) \\ 
+KOSI07 F omega-global-gamma4 rates-one & 1883.0 & -24967.2 & 63 (3 + 60) \\ 
+KOSI07 F omega-global-one rates-gamma4 & 2378.8 & -25215.1 & 63 (3 + 60) \\ 
+GY94 CF3x4 omega-global-one rates-one & 2544.5 & -25350.0 & 11 (2 + 9) \\ 
+KOSI07 F omega-global-one rates-one & 3040.0 & -25546.7 & 62 (2 + 60) \\ 
+combined-FracToleratedrandomized & 5632.8 & -26905.1 & 0 (0 + 0) \\ 
+replicate 1-FracToleratedrandomized & 6002.4 & -27089.9 & 0 (0 + 0) \\ 
+replicate 3-FracToleratedrandomized & 6138.8 & -27158.1 & 0 (0 + 0) \\ 
+replicate 2-FracToleratedrandomized & 6477.8 & -27327.6 & 0 (0 + 0) \\ 
+combined-HalpernBrunorandomized & 7072.8 & -27625.1 & 0 (0 + 0) \\ 
+replicate 1-HalpernBrunorandomized & 7795.0 & -27986.2 & 0 (0 + 0) \\ 
+replicate 3-HalpernBrunorandomized & 7891.8 & -28034.6 & 0 (0 + 0) \\ 
+replicate 2-HalpernBrunorandomized & 8494.4 & -28335.9 & 0 (0 + 0) 
+\end{tabular}

examples/2014Analysis_Influenza_H1_HA/H1_HumanSwine_KOSI07_summary.csv

@@ -0,0 +1,27 @@
+#Summary for tree H1_HumanSwine_KOSI07.
+#
+#SUBSTITUTION_MODEL, dAIC, LOG_LIKELIHOOD, FREE_PARAMETERS, MAXIMUM_LIKELIHOOD_PARAMETERS, EMPIRICAL_PARAMETERS
+combined-FracTolerated, 0, -24082.5, 0, 0, 0
+replicate_3-FracTolerated, 304.8, -24234.9, 0, 0, 0
+combined-HalpernBruno, 494.4, -24329.7, 0, 0, 0
+replicate_1-FracTolerated, 534.2, -24349.6, 0, 0, 0
+replicate_3-HalpernBruno, 653.2, -24409.1, 0, 0, 0
+replicate_2-FracTolerated, 869.4, -24517.2, 0, 0, 0
+GY94_CF3x4_omega-global-gamma4_rates-gamma4, 876.673, -24507.8, 13, 4, 9
+replicate_1-HalpernBruno, 976.8, -24570.9, 0, 0, 0
+GY94_CF3x4_omega-global-gamma4_rates-one, 1100.99, -24621, 12, 3, 9
+replicate_2-HalpernBruno, 1180.4, -24672.7, 0, 0, 0
+KOSI07_F_omega-global-gamma4_rates-gamma4, 1609.02, -24823, 64, 4, 60
+GY94_CF3x4_omega-global-one_rates-gamma4, 1856.23, -24998.6, 12, 3, 9
+KOSI07_F_omega-global-gamma4_rates-one, 1867.29, -24953.1, 63, 3, 60
+KOSI07_F_omega-global-one_rates-gamma4, 2367.9, -25203.4, 63, 3, 60
+GY94_CF3x4_omega-global-one_rates-one, 2548.27, -25345.6, 11, 2, 9
+KOSI07_F_omega-global-one_rates-one, 3027.99, -25534.5, 62, 2, 60
+combined-FracToleratedrandomized, 5628, -26896.5, 0, 0, 0
+replicate_1-FracToleratedrandomized, 5993.6, -27079.3, 0, 0, 0
+replicate_3-FracToleratedrandomized, 6138, -27151.5, 0, 0, 0
+replicate_2-FracToleratedrandomized, 6475.2, -27320.1, 0, 0, 0
+combined-HalpernBrunorandomized, 7069.4, -27617.2, 0, 0, 0
+replicate_1-HalpernBrunorandomized, 7786.8, -27975.9, 0, 0, 0
+replicate_3-HalpernBrunorandomized, 7889.2, -28027.1, 0, 0, 0
+replicate_2-HalpernBrunorandomized, 8496, -28330.5, 0, 0, 0

examples/2014Analysis_Influenza_H1_HA/H1_HumanSwine_KOSI07_summary.tex

@@ -0,0 +1,27 @@
+\begin{tabular}{c|c|c|c}
+model & $\Delta$AIC & log likelihood & \parbox[b]{0.9in}{\center parameters (optimized + empirical)} \\ \hline
+combined-FracTolerated & 0.0 & -24082.5 & 0 (0 + 0) \\ 
+replicate 3-FracTolerated & 304.8 & -24234.9 & 0 (0 + 0) \\ 
+combined-HalpernBruno & 494.4 & -24329.7 & 0 (0 + 0) \\ 
+replicate 1-FracTolerated & 534.2 & -24349.6 & 0 (0 + 0) \\ 
+replicate 3-HalpernBruno & 653.2 & -24409.1 & 0 (0 + 0) \\ 
+replicate 2-FracTolerated & 869.4 & -24517.2 & 0 (0 + 0) \\ 
+GY94 CF3x4 omega-global-gamma4 rates-gamma4 & 876.7 & -24507.8 & 13 (4 + 9) \\ 
+replicate 1-HalpernBruno & 976.8 & -24570.9 & 0 (0 + 0) \\ 
+GY94 CF3x4 omega-global-gamma4 rates-one & 1101.0 & -24621.0 & 12 (3 + 9) \\ 
+replicate 2-HalpernBruno & 1180.4 & -24672.7 & 0 (0 + 0) \\ 
+KOSI07 F omega-global-gamma4 rates-gamma4 & 1609.0 & -24823.0 & 64 (4 + 60) \\ 
+GY94 CF3x4 omega-global-one rates-gamma4 & 1856.2 & -24998.6 & 12 (3 + 9) \\ 
+KOSI07 F omega-global-gamma4 rates-one & 1867.3 & -24953.1 & 63 (3 + 60) \\ 
+KOSI07 F omega-global-one rates-gamma4 & 2367.9 & -25203.4 & 63 (3 + 60) \\ 
+GY94 CF3x4 omega-global-one rates-one & 2548.3 & -25345.6 & 11 (2 + 9) \\ 
+KOSI07 F omega-global-one rates-one & 3028.0 & -25534.5 & 62 (2 + 60) \\ 
+combined-FracToleratedrandomized & 5628.0 & -26896.5 & 0 (0 + 0) \\ 
+replicate 1-FracToleratedrandomized & 5993.6 & -27079.3 & 0 (0 + 0) \\ 
+replicate 3-FracToleratedrandomized & 6138.0 & -27151.5 & 0 (0 + 0) \\ 
+replicate 2-FracToleratedrandomized & 6475.2 & -27320.1 & 0 (0 + 0) \\ 
+combined-HalpernBrunorandomized & 7069.4 & -27617.2 & 0 (0 + 0) \\ 
+replicate 1-HalpernBrunorandomized & 7786.8 & -27975.9 & 0 (0 + 0) \\ 
+replicate 3-HalpernBrunorandomized & 7889.2 & -28027.1 & 0 (0 + 0) \\ 
+replicate 2-HalpernBrunorandomized & 8496.0 & -28330.5 & 0 (0 + 0) 
+\end{tabular}